From b99a7bdd254eb579d1ad57a08ec7166fc74b1ce6 Mon Sep 17 00:00:00 2001
From: nikhil153 <nikhil153@gmail.com>
Date: Mon, 1 Sep 2025 21:03:59 -0400
Subject: [PATCH 1/3] Suggested modifications to directory layout of the
 bids-study DatasetType

---
 src/schema/rules/directories.yaml | 20 +++++++++++++++-----
 1 file changed, 15 insertions(+), 5 deletions(-)

diff --git a/src/schema/rules/directories.yaml b/src/schema/rules/directories.yaml
index e5415e8c14..857dcbee2c 100644
--- a/src/schema/rules/directories.yaml
+++ b/src/schema/rules/directories.yaml
@@ -16,14 +16,16 @@
 # The special "root" specifier describes the root of the dataset and only defines subdirectories.
 # No naming convention applies, and the requirement level and opacity would be superfluous.
 #
-study:
+bids-study:
   root:
     subdirs:
       - code
       - docs
-      - derivatives
+      - bids-raw
+      - bids-derivatives
       - logs
       - sourcedata
+      - phenotype
   code:
     name: code
     level: optional
@@ -32,7 +34,11 @@ study:
     name: docs
     level: optional
     opaque: true
-  derivatives:
+  bids-raw:
+    name: bids-raw
+    level: optional
+    opaque: true
+  bids-derivatives:
     name: derivatives
     level: optional
     opaque: true
@@ -44,8 +50,12 @@ study:
     name: sourcedata
     level: optional
     opaque: true
+  phenotype:
+    name: phenotype
+    level: optional
+    opaque: false
 
-raw:
+bids-raw:
   root:
     subdirs:
       - code
@@ -103,7 +113,7 @@ raw:
     level: required
     opaque: false
 
-derivative:
+bids-derivative:
   root:
     subdirs:
       - code

From 2d591985c4b79d8009c51914800b079bb0a6ce9a Mon Sep 17 00:00:00 2001
From: nikhil153 <nikhil153@gmail.com>
Date: Mon, 1 Sep 2025 22:51:11 -0400
Subject: [PATCH 2/3] fixed minor typos

---
 src/schema/rules/directories.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/rules/directories.yaml b/src/schema/rules/directories.yaml
index 857dcbee2c..1dbedf4475 100644
--- a/src/schema/rules/directories.yaml
+++ b/src/schema/rules/directories.yaml
@@ -39,7 +39,7 @@ bids-study:
     level: optional
     opaque: true
   bids-derivatives:
-    name: derivatives
+    name: bids-derivatives
     level: optional
     opaque: true
   logs:

From e0fe3ce304980cba4af020bd976223f2b4dce523 Mon Sep 17 00:00:00 2001
From: nikhil153 <nikhil153@gmail.com>
Date: Wed, 10 Sep 2025 13:45:11 -0400
Subject: [PATCH 3/3] removed bids prefix from the DatasetType and subdirs.

---
 src/schema/rules/directories.yaml | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/schema/rules/directories.yaml b/src/schema/rules/directories.yaml
index 1dbedf4475..c2842619cd 100644
--- a/src/schema/rules/directories.yaml
+++ b/src/schema/rules/directories.yaml
@@ -16,13 +16,13 @@
 # The special "root" specifier describes the root of the dataset and only defines subdirectories.
 # No naming convention applies, and the requirement level and opacity would be superfluous.
 #
-bids-study:
+study:
   root:
     subdirs:
       - code
       - docs
-      - bids-raw
-      - bids-derivatives
+      - rawdata
+      - derivatives
       - logs
       - sourcedata
       - phenotype
@@ -34,12 +34,12 @@ bids-study:
     name: docs
     level: optional
     opaque: true
-  bids-raw:
-    name: bids-raw
+  rawdata:
+    name: rawdata
     level: optional
     opaque: true
-  bids-derivatives:
-    name: bids-derivatives
+  derivatives:
+    name: derivatives
     level: optional
     opaque: true
   logs:
@@ -55,7 +55,7 @@ bids-study:
     level: optional
     opaque: false
 
-bids-raw:
+raw:
   root:
     subdirs:
       - code
@@ -113,7 +113,7 @@ bids-raw:
     level: required
     opaque: false
 
-bids-derivative:
+derivative:
   root:
     subdirs:
       - code